The biggest issue I had during the beta-testing phase was that iMovie wouldn't launch (though iDVD, long discontinued, worked perfectly -- what the --), and that during Beta 1 my preferred FTP programs and Safari extensions didn't work. All sorted in due course obviously, that's why they call it a beta.
I'm not meaning to make it sound like Yosemite is without flaw, just passing on my real-world experience with it from the early betas to present. Since I didn't (nor could) test all possible apps and scenarios, there's still plenty of room for problems I continue to be unaware of, but for me and my intensive internet/writing/editing/audio work, it ran so well I was sorely tempted to make it my primary OS by beta 3.